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Expression Database
GUDMAP:7091
Theiler Stage
TS23
Supplemental Data Files
CEL file:
OuterUB_1_1_6_06_MOE430.2.CEL
CHP file:
OuterUB_1_1_6_06_MOE430.2.CHP
RPT file:
OuterUB_1_1_6_06_MOE430.2.RPT
TXT file:
OuterUB_1_1_6_06_MOE430.2.TXT
Archive ID
38
Principal Investigator(s)
Steve Potter,
Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, steve.potter@cchmc.org
Submitted By
Eric Brunskill,
Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA, brune0@cchmc.org
Specimen Details
Sample GEO ID:
GSM144599
Sample Description:
E15.5 Ureteric tip with flanking cortical collecting duct before first branch
Title:
OuterUB_1_1_6_06
Component(s) Sampled:
ureteric tip (EMAP:27752)
Organism:
Mus musculus
Strain:
CD-1
Genotype:
Wild type
Sex:
Unknown
Development Age:
15.5 dpc
Theiler Stage:
23
Pool Size:
Approx 50 sections from 5 kidneys
Pooled Sample:
Yes
Dissection Method:
Laser capture microdissection
Experimental Design:
CD-1 mice are time-mated. Pregnant CD-1 mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses placed in OCT in a mold, frozen in liquid nitrogen and stored at -80°C. Blocks are sectioned, stained and used for laser capture micro-dissection.
Array Hybridization
Extracted Molecule:
Total RNA
A260:280 Ratio:
NA
RNA Extraction Protocol:
Potter protocol: 'RNA purification'
Target Amplification Manufacturer/kit:
TargetAmp 2-Round Aminoallyl-aRNA Amplification Kit 1.0 (EPICENTRE Biotechnologies)
Target Amplification Protocol:
Potter protocols
Rounds of Amplification:
2
Amount Labeled Target Hybridized To Array:
5ug
Label:
Biotin
Label Protocol:
Biotin-X-X-NHS (EPICENTRE Biotechnologies)
Array Hyb/Wash Protocol:
Affymetrix Standard Protocol.
Scan Protocol:
GCOS Tgt Value:
1500
Data Analysis Method:
Affymetrix GCOS and Gene Spring and Avadis programs
Reference:
PND 0.5 whole embryo RNA
Series Details
Series GEO ID:
GSE6290
Number of Samples:
37 samples
Title:
Gene expression profiles of components isolated from developing kidney at E11.5, E12.5 & E15.5 using LCM. (GUDMAP Series ID: 10)
Summary:
The long term objective is to create an encyclopedia of the expression levels of all genes in multiple components of the developing kidney. The central thesis is straightforward. The combination of laser capture microdissection (LCM) plus microarray analysis offers a powerful, efficient and effective method for the creation of a global gene expression atlas of the developing kidney. Microarrays with essentially complete genome coverage can be used to quantitate expression levels of every gene in laser capture microdissected components of the developing kidney. The ensuing rapid read-out provides an expression atlas that is more sensitive, more economical and more complete than would be possible by in situ hybridizations alone.
Type:
Comparison of kidney components.
Overall Design:
At different developmental time points we isolate discrete elements of the kidney by using laser capture microdissection and then define their gene expression profiles with microarrays.
Platform Details
Platform GEO ID:
GPL1261
Title:
Affymetrix GeneChip Mouse Genome 430 2.0 Array
Distribution:
commercial
Technology:
in situ oligonucleotide
Organism:
Mus musculus
Manufacturer:
Affymetrix
Manufacturer Protocol:
N/A
Catalogue Number:
N/A
